Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001782.1 Hibiscus syriacus cultivar Beakdansim tig00003599_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47336
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2399 original size:20 final size:20
Alignment explanation
Indices: 2374--2422 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
2364 TTGGGGGGTC
*
2374 TGAAAATCGCTTGATTCGAT
1 TGAAAATCGCCTGATTCGAT
2394 TGAAAATATCGCCTGATTCGAT
1 TG-AAA-ATCGCCTGATTCGAT
2416 TGAAAAT
1 TGAAAAT
2423 ATCGCTTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 6 0.23
22 16 0.62
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
TGAAAATCGCCTGATTCGAT
Found at i:2410 original size:22 final size:22
Alignment explanation
Indices: 2379--2427 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2369 GGGTCTGAAA
*
2379 ATCGCTTGATTCGATTGAAAAT
1 ATCGCCTGATTCGATTGAAAAT
2401 ATCGCCTGATTCGATTGAAAAT
1 ATCGCCTGATTCGATTGAAAAT
2423 ATCGC
1 ATCGC
2428 TTCTGCCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (22 bp):
ATCGCCTGATTCGATTGAAAAT
Found at i:3587 original size:2 final size:2
Alignment explanation
Indices: 3580--3605 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3570 TCATTACATT
3580 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3606 CTTTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15111 original size:37 final size:37
Alignment explanation
Indices: 15065--15273 Score: 197
Period size: 37 Copynumber: 5.8 Consensus size: 37
15055 GAAGAAATAG
15065 AAAAAATGAAAAAATAAAAAAAATGAAAAAAATGAAA
1 AAAAAATGAAAAAATAAAAAAAATGAAAAAAATGAAA
*
15102 AAAAAATGAAAAAAATGAAAAAAATG-AAAAAATGAAA
1 AAAAAATG-AAAAAATAAAAAAAATGAAAAAAATGAAA
* *
15139 AGAAAATGAAGAAAAT-GAAAAAAT-AAAAAAAT-AAA
1 AAAAAATGAA-AAAATAAAAAAAATGAAAAAAATGAAA
* *
15174 AAAAAAAGAAAAAA-AAATAAAATGAAATGAAAAATGAAA
1 AAAAAATGAAAAAATAAAAAAAATG-AA--AAAAATGAAA
* * * **
15213 AAAGAA-G-AAAGAGAAAAAAAATG-AAAAAATGATG
1 AAAAAATGAAAAAATAAAAAAAATGAAAAAAATGAAA
15247 AAAAAA-G-AAAAATAAAAAGAAAT-AAAA
1 AAAAAATGAAAAAATAAAAA-AAATGAAAA
15274 GGGGGGTTCA
Statistics
Matches: 145, Mismatches: 15, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
34 33 0.23
35 18 0.12
36 19 0.13
37 35 0.24
38 32 0.22
39 8 0.06
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (37 bp):
AAAAAATGAAAAAATAAAAAAAATGAAAAAAATGAAA
Found at i:15132 original size:46 final size:45
Alignment explanation
Indices: 15066--15264 Score: 159
Period size: 46 Copynumber: 4.4 Consensus size: 45
15056 AAGAAATAGA
15066 AAAAATGAAAAAATAAAAAAAATG--AAAAAAATGAAAAAAAAATGAA
1 AAAAATGAAAAAAT-AAAAAAATGAAAAAAAAATG--AAAAAAATGAA
* * *
15112 AAAAATGAAAAAAATGAAAAAATGAAAAGAAAATGAAGAAAATGAA
1 AAAAATG-AAAAAATAAAAAAATGAAAAAAAAATGAAAAAAATGAA
* *
15158 AA-AATAAAAAAATAAAAAAAAAAGAAAAAAAAAT-AAAATGAAATG--
1 AAAAATGAAAAAAT--AAAAAAATGAAAAAAAAATGAAAA--AAATGAA
* *
15203 AAAAATGAAAAAA-GAAGAAA-GAGAAAAAAAATG-AAAAAATGATGA
1 AAAAATGAAAAAATAAAAAAATGA-AAAAAAAATGAAAAAAATGA--A
15248 AAAAA-G-AAAAATAAAAA
1 AAAAATGAAAAAATAAAAA
15265 GAAATAAAAG
Statistics
Matches: 125, Mismatches: 13, Indels: 32
0.74 0.08 0.19
Matches are distributed among these distances:
41 5 0.04
42 2 0.02
43 22 0.18
44 11 0.09
45 13 0.10
46 52 0.42
47 12 0.10
48 8 0.06
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (45 bp):
AAAAATGAAAAAATAAAAAAATGAAAAAAAAATGAAAAAAATGAA
Found at i:15188 original size:9 final size:9
Alignment explanation
Indices: 15052--15274 Score: 97
Period size: 9 Copynumber: 24.4 Consensus size: 9
15042 TATTTCGCTT
*
15052 AAAGAAGAA
1 AAAGAAAAA
*
15061 ATAG-AAAA
1 AAAGAAAAA
*
15069 AATGAAAAA
1 AAAGAAAAA
*
15078 ATA-AAAAA
1 AAAGAAAAA
*
15086 AATGAAAAA
1 AAAGAAAAA
*
15095 AATGAAAAAA
1 AAAG-AAAAA
15105 AAATGAAAAA
1 AAA-GAAAAA
*
15115 AATGAAAAA
1 AAAGAAAAA
*
15124 AATG-AAAA
1 AAAGAAAAA
*
15132 AATGAAAAGA
1 AAAGAAAA-A
*
15142 AAATGAAGAA
1 AAA-GAAAAA
*
15152 AATGAAAAA
1 AAAGAAAAA
15161 ATAA-AAAAA
1 A-AAGAAAAA
*
15170 TAA-AAAAA
1 AAAGAAAAA
15178 AAAG-AAAA
1 AAAGAAAAA
*
15186 AAA-AATAA
1 AAAGAAAAA
*
15194 AATGAAATGAA
1 AAAGAAA--AA
15205 AAATG--AAA
1 AAA-GAAAAA
*
15213 AAAGAAGAA
1 AAAGAAAAA
*
15222 AGAGAAAAA
1 AAAGAAAAA
15231 AAATGAAAAA
1 AAA-GAAAAA
*
15241 ATGATGAAAAA
1 A--AAGAAAAA
15252 AGAA-AAATAA
1 A-AAGAAA-AA
*
15262 AAAGAAATA
1 AAAGAAAAA
15271 AAAG
1 AAAG
15275 GGGGGTTCAA
Statistics
Matches: 165, Mismatches: 28, Indels: 42
0.70 0.12 0.18
Matches are distributed among these distances:
7 1 0.01
8 45 0.27
9 64 0.39
10 37 0.22
11 16 0.10
12 2 0.01
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:15207 original size:83 final size:77
Alignment explanation
Indices: 15052--15273 Score: 227
Period size: 83 Copynumber: 2.7 Consensus size: 77
15042 TATTTCGCTT
* *
15052 AAAGAAG-AAATAGAAAAAATGAAAAAATAAAAAAAATGAAAAAAATGAAAAAAAAATGAAAAAA
1 AAAGAAGAAAAT-GAAAAAATGAAAAAATAAAAAAAA-AAAAAAAAAGAAAAAAAAATGAAAAAA
15116 ATGAAAAAAATGAAA
64 ATG-AAAAAATGAAA
15131 AAATGAAAAGAAAATGAAGAAAATGAAAAAATAAAAAAATAAAAAAAAAAGAAAAAAAAAT-AAA
1 AAA-G--AAGAAAATGAA-AAAATGAAAAAATAAAAAAA-AAAAAAAAAAGAAAAAAAAATGAAA
15195 ATGAAATG-AAAAATGAAA
61 A--AAATGAAAAAATGAAA
*
15213 AAAGAAGAAAGA-GAAAAAAAATGAAAAAATGATGAAAAAAGAAAAATAAAAAGAAATAAAA
1 AAAGAAGAAA-ATG--AAAAAATGAAAAAAT-A--AAAAAA-AAAAA-AAAAAGAAAAAAAA
15274 GGGGGGTTCA
Statistics
Matches: 124, Mismatches: 4, Indels: 25
0.81 0.03 0.16
Matches are distributed among these distances:
79 10 0.08
80 15 0.12
81 4 0.03
82 23 0.19
83 53 0.43
84 19 0.15
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (77 bp):
AAAGAAGAAAATGAAAAAATGAAAAAATAAAAAAAAAAAAAAAAAGAAAAAAAAATGAAAAAAAT
GAAAAAATGAAA
Found at i:15228 original size:28 final size:25
Alignment explanation
Indices: 15066--15241 Score: 117
Period size: 28 Copynumber: 6.5 Consensus size: 25
15056 AAGAAATAGA
*
15066 AAAAATG-AAAAAATAAAAAAAATG
1 AAAAATGAAAAAAAAAAAAAAAATG
15090 AAAAAAATGAAAAAAAAATGAAAAAAATG
1 --AAAAATGAAAAAAAAA--AAAAAAATG
* *
15119 AAAAAAATGAAAAAATGAAAAGAAAATG
1 --AAAAATGAAAAAA-AAAAAAAAAATG
*
15147 AAGAAAATGAAAAAATAAAAAAATAAA-A
1 -A-AAAATGAAAAAA-AAAAAAA-AAATG
*
15175 AAAAAAGAAAAAAAAATAAAATGAAATG
1 AAAAATGAAAAAAAAA-AAAA--AAATG
*
15203 AAAAATGAAAAAAGAAGAAAGAGAAA--
1 AAAAATGAAAAAA-AA-AAA-AAAAATG
15229 AAAAATGAAAAAA
1 AAAAATGAAAAAA
15242 TGATGAAAAA
Statistics
Matches: 127, Mismatches: 11, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
25 3 0.02
26 35 0.28
27 13 0.10
28 41 0.32
29 31 0.24
30 4 0.03
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (25 bp):
AAAAATGAAAAAAAAAAAAAAAATG
Found at i:16597 original size:37 final size:37
Alignment explanation
Indices: 16547--16622 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
16537 AAACAATTCA
16547 ATCTTAAGCCTTCACGGAAGAGTAGTGAACAAAA-TC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAACAAAACTC
* *
16583 ATCTATAAGGCTTCACGGAAGAGTAGTGAAGAAAACTC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAACAAAACTC
16621 AT
1 AT
16623 TTTATGAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 4 0.11
37 28 0.78
38 4 0.11
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.22
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAACAAAACTC
Found at i:16694 original size:55 final size:54
Alignment explanation
Indices: 16633--16999 Score: 470
Period size: 55 Copynumber: 6.7 Consensus size: 54
16623 TTTATGAAGA
* * *
16633 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTAGTTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTA-TTGAAGATTGT
* * *
16688 TTGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACATTCACTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTT-ATTGAAGATTGT
* *
16743 TCGAGT-TCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACG-TTATTGAAGATTGT
** *
16798 TCGAGTCTTATACTCCCTGAAATAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACG-TTATTGAAGATTGT
* *
16853 TCGAGT-TCTATACTCCCTGAACGAATAGGGAGCAAACCCGTTTATTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACG-TTATTGAAGATTGT
* * *
16908 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTT-TGCCGAAGTTTGT
1 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTAT--TGAAGATTGT
* *
16963 TCTAGTCTTATACTCCCTGAAGGAATAGGGAGCAGAC
1 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGAC
17000 TTATCATTTG
Statistics
Matches: 276, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
53 1 0.00
54 4 0.01
55 266 0.96
56 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (54 bp):
TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTATTGAAGATTGT
Found at i:16826 original size:110 final size:110
Alignment explanation
Indices: 16633--16999 Score: 533
Period size: 110 Copynumber: 3.3 Consensus size: 110
16623 TTTATGAAGA
* * * * *
16633 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACG-TTAGTTGAAGATTGTTTGAGTCTT
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTTA-TTGAAGATTGTTCGAGTCTT
** * **
16697 ATACTCCCTGAACGAATAGGGAGCAGACACATTCACTGAAGATTGT
65 ATACTCCCTGAAATAATAGGGAGCAGACACGTTTGCTGAAGATTGT
*
16743 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTCTTA
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTTA
*
16808 TACTCCCTGAAATAATAGGGAGCAGACACGTTTGTTGAAGATTGT
66 TACTCCCTGAAATAATAGGGAGCAGACACGTTTGCTGAAGATTGT
*
16853 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCAAACCCGTTTATTGAAGATTGTTCGAGTCTTA
1 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTTA
* *
16918 TACTCCCTG-AATGAATAGGGAGCAGACACGTTTGCCGAAGTTTGT
66 TACTCCCTGAAAT-AATAGGGAGCAGACACGTTTGCTGAAGATTGT
* *
16963 TCTAG-TCTTATACTCCCTGAAGGAATAGGGAGCAGAC
1 TCGAGTTC-TATACTCCCTGAACGAATAGGGAGCAGAC
17000 TTATCATTTG
Statistics
Matches: 234, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
109 5 0.02
110 226 0.97
111 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (110 bp):
TCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTTA
TACTCCCTGAAATAATAGGGAGCAGACACGTTTGCTGAAGATTGT
Found at i:16905 original size:165 final size:165
Alignment explanation
Indices: 16633--16999 Score: 531
Period size: 165 Copynumber: 2.2 Consensus size: 165
16623 TTTATGAAGA
* * *
16633 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTAGTTGAAGATTGTTTGAGTCTTA
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTAGTTGAAGATTGTTCGAGTCTTA
*
16698 TACTCCCTGAACGAATAGGGAGCAGACACATTCACTGAAGATTGTTCGAGT-TCTATACTCCCTG
66 TACTCCCTGAACGAATAGGGAGCAAACACATTCACTGAAGATTGTTCGAGTCT-TATACTCCCTG
* * **
16762 AACGAATAGGGAGCGGACCCGTTTATTGAAGATTGT
130 AACGAATAGGGAGCAGACACGTTTACCGAAGATTGT
* *
16798 TCGAGTCTTATACTCCCTGAAATAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCGAGT-TCT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTAGTTGAAGATTGTTCGAGTCT-T
* * * *
16862 ATACTCCCTGAACGAATAGGGAGCAAACCCGTTTATTGAAGATTGTTCGAGTCTTATACTCCCTG
65 ATACTCCCTGAACGAATAGGGAGCAAACACATTCACTGAAGATTGTTCGAGTCTTATACTCCCTG
* * *
16927 AATGAATAGGGAGCAGACACGTTTGCCGAAGTTTGT
130 AACGAATAGGGAGCAGACACGTTTACCGAAGATTGT
* *
16963 TCTAGTCTTATACTCCCTGAAGGAATAGGGAGCAGAC
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAC
17000 TTATCATTTG
Statistics
Matches: 180, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
164 1 0.01
165 178 0.99
166 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (165 bp):
TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTAGTTGAAGATTGTTCGAGTCTTA
TACTCCCTGAACGAATAGGGAGCAAACACATTCACTGAAGATTGTTCGAGTCTTATACTCCCTGA
ACGAATAGGGAGCAGACACGTTTACCGAAGATTGT
Found at i:19346 original size:15 final size:15
Alignment explanation
Indices: 19326--19363 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
19316 ATAAATCAAA
*
19326 TCAAGTTCGGATTTG
1 TCAAGTTCGAATTTG
19341 TCAAGTTCGAATTTG
1 TCAAGTTCGAATTTG
19356 TCAAGTTC
1 TCAAGTTC
19364 AATGCAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (15 bp):
TCAAGTTCGAATTTG
Found at i:20888 original size:43 final size:43
Alignment explanation
Indices: 20760--20894 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 43
20750 TGAGAACCAA
* * * * *
20760 AAACGCCGCCATAGTTCAAGATCTATAGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGAAC
*
20803 AAA---CGCAAAAGGTCAAGATCTATAGCGGCGTGTTTT-GAAC
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCGT-TTTTGGAAC
* *
20843 AAACGCCGCAAAAGGT-TAGATATTTAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGA-AC
20886 AAACGCCGC
1 AAACGCCGC
20895 TAATTACCAT
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
40 31 0.39
41 8 0.10
42 16 0.20
43 24 0.30
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGAAC
Found at i:24339 original size:83 final size:84
Alignment explanation
Indices: 24205--24686 Score: 420
Period size: 82 Copynumber: 5.9 Consensus size: 84
24195 TTTAAATTTT
* * * * * * * * *
24205 CGGCGTTTGTA-ACACAAACGCCATTAAAGTACAAGTTTTTCA-TGGCATTTGTTTAAAAATGCC
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTAT-AGCGGCGTTTGTATAAAAACGCC
*
24268 ACTAAAGTACAAGTTTATAG
65 ACTAAAGTACGAGTTTATAG
* * * * **
24288 C-GCGTTTGTAAACAAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTA-AAAAATACCA
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
*
24351 CTAAAGTACGAGTCTATAG
66 CTAAAGTACGAGTTTATAG
* * *
24370 CGGCGTTTATA-AAAAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAAAAACGCC
1 CGGCGTTTGTATACAAAAA-CGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
*
24434 ACTAAAGTATGAG-TTATAG
65 ACTAAAGTACGAGTTTATAG
* * * * * * *
24453 CGGCGTTTTTATAC--AAACGCCACTACAGTACGACT-TATAACAGTGCTTTTATAAAAAAACGC
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTATAGC-G-GCGTTTGTATAAAAACGC
*
24515 CACTAAAGTACGAGTCT-TAG
64 CACTAAAGTACGAGTTTATAG
* * * *
24535 CGGCGTTTGTATA-AAAAACGCTC-CTAAAGTATGATTCTATAGCGGAGTTTGTGTAAAAACGCC
1 CGGCGTTTGTATACAAAAACGC-CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* *
24598 ACTATAGTACTAGTCTT-TAG
65 ACTAAAGTACGAGT-TTATAG
* * * * * * *
24618 CGGCGTTTGTATAC-AAAA-GCCACTAAAGTAAGA-TCTTTTGCGGCCTTTTTATACAAACGCCT
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
24680 CTAAAGT
66 CTAAAGT
24687 TAGATCTTTT
Statistics
Matches: 327, Mismatches: 56, Indels: 34
0.78 0.13 0.08
Matches are distributed among these distances:
80 5 0.02
81 45 0.14
82 126 0.39
83 125 0.38
84 26 0.08
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (84 bp):
CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTACGAGTTTATAG
Found at i:24345 original size:82 final size:84
Alignment explanation
Indices: 24205--24647 Score: 398
Period size: 83 Copynumber: 5.4 Consensus size: 84
24195 TTTAAATTTT
* * * * * * * ** *
24205 CGGCGTTTGTA-ACACAAACGCCATTAAAGTACAAGTTTTTCA-TGGCATTTGTTTAAAAATGCC
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTAT-AGCGGCGTTTGTAAAAAAACGCC
*
24268 ACTAAAGTACAAGTTTATAG
65 ACTAAAGTACGAGTTTATAG
* * * *
24288 C-GCGTTTGTAAACAAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTAAAAAATA--CC
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAAAAA-ACGCC
*
24350 ACTAAAGTACGAGTCTATAG
65 ACTAAAGTACGAGTTTATAG
* *
24370 CGGCGTTTATA-AAAAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTG-AATAAAAACGC
1 CGGCGTTTGTATACAAAAA-CGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAA-AAAAACGC
*
24433 CACTAAAGTATGAG-TTATAG
64 CACTAAAGTACGAGTTTATAG
* * * * * *
24453 CGGCGTTTTTATAC--AAACGCCACTACAGTACGACT-TATAACAGTGCTTTTATAAAAAAACGC
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTATAGC-G-GCGTTTGTAAAAAAACGC
*
24515 CACTAAAGTACGAGTCT-TAG
64 CACTAAAGTACGAGTTTATAG
* * * **
24535 CGGCGTTTGTATA-AAAAACGCTC-CTAAAGTATGATTCTATAGCGGAGTTTGTGTAAAAACGCC
1 CGGCGTTTGTATACAAAAACGC-CACTAAAGTACGAGTCTATAGCGGCGTTTGTAAAAAAACGCC
* *
24598 ACTATAGTACTAGTCTT-TAG
65 ACTAAAGTACGAGT-TTATAG
24618 CGGCGTTTGTATAC-AAAA-GCCACTAAAGTA
1 CGGCGTTTGTATACAAAAACGCCACTAAAGTA
24648 AGATCTTTTG
Statistics
Matches: 299, Mismatches: 41, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
80 5 0.02
81 18 0.06
82 120 0.40
83 134 0.45
84 22 0.07
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (84 bp):
CGGCGTTTGTATACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAAAAAACGCCA
CTAAAGTACGAGTTTATAG
Found at i:24362 original size:40 final size:39
Alignment explanation
Indices: 24205--24661 Score: 275
Period size: 41 Copynumber: 11.1 Consensus size: 39
24195 TTTAAATTTT
* * *
24205 CGGCGTTTGTAACACAAACGCCATTAAAGTACAAGTTTTTCA-
1 CGGCGTTTGTAA-A-AAA-GCCACTAAAGTACGAGTCTTT-AG
* * * *
24247 TGGCATTTGTTTAAAAATGCCACTAAAGTACAAGT-TTATAG
1 CGGCGTTTG--TAAAAAAGCCACTAAAGTACGAGTCTT-TAG
* *
24288 C-GCGTTTGTAAACAAAAACGCCACGAAAGAACGAGTCTTTAG
1 CGGCGTTTGT--A-AAAAA-GCCACTAAAGTACGAGTCTTTAG
* *
24330 CGGCGTTTGTAAAAAATACCACTAAAGTACGAGTCTATAG
1 CGGCGTTTGTAAAAAA-GCCACTAAAGTACGAGTCTTTAG
* *
24370 CGGCGTTTATAAAAAAAATCGCCACTAAAGTACGAGTCTATAG
1 CGGCGTTTGT--AAAAAA--GCCACTAAAGTACGAGTCTTTAG
* * *
24413 CGGCGTTTGAATAAAAACGCCACTAAAGTATGAGT-TATAG
1 CGGCGTTTG--TAAAAAAGCCACTAAAGTACGAGTCTTTAG
* * * *
24453 CGGCGTTTTTATACAAACGCCACTACAGTACGA--CTTATAA
1 CGGCGTTTGTA-A-AAAAGCCACTAAAGTACGAGTCTT-TAG
* *
24493 CAGTGCTTTTATAAAAAAACGCCACTAAAGTACGAGTC-TTAG
1 C-G-GCGTTTGT-AAAAAA-GCCACTAAAGTACGAGTCTTTAG
* * *
24535 CGGCGTTTGTATAAAAAACGCTC-CTAAAGTATGATTCTATAG
1 CGGCGTTTG--TAAAAAA-GC-CACTAAAGTACGAGTCTTTAG
* * * *
24577 CGGAGTTTGTGTAAAAACGCCACTATAGTACTAGTCTTTAG
1 CGGCG-TT-TGTAAAAAAGCCACTAAAGTACGAGTCTTTAG
* *
24618 CGGCGTTTGTATACAAAAGCCACTAAAGTAAGA-TCTTTTG
1 CGGCGTTTGTA-A-AAAAGCCACTAAAGTACGAGTCTTTAG
24658 CGGC
1 CGGC
24662 CTTTTTATAC
Statistics
Matches: 332, Mismatches: 49, Indels: 70
0.74 0.11 0.16
Matches are distributed among these distances:
38 3 0.01
39 6 0.02
40 95 0.29
41 99 0.30
42 72 0.22
43 50 0.15
44 6 0.02
45 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (39 bp):
CGGCGTTTGTAAAAAAGCCACTAAAGTACGAGTCTTTAG
Found at i:24563 original size:41 final size:42
Alignment explanation
Indices: 24259--24686 Score: 402
Period size: 40 Copynumber: 10.4 Consensus size: 42
24249 GCATTTGTTT
* * * *
24259 AAAAATGCCACTAAAGTACAAGTTTATAGC-GCGTTTGTAAA
1 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* * *
24300 CAAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTA-A
1 -AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* *
24342 AAAATA--CCACTAAAGTACGAGTCTATAGCGGCGTTTATAAA
1 AAAA-ACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
*
24383 AAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGAAT-
1 AAAAA-CGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* *
24425 AAAAACGCCACTAAAGTATGAGT-TATAGCGGCGTTTTTAT-
1 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* * * *
24465 ACAAACGCCACTACAGTACGACT-TATAACAGTGC-TTT-TATAA
1 AAAAACGCCACTAAAGTACGAGTCTATAGC-G-GCGTTTGTAT-A
24507 AAAAACGCCACTAAAGTACGAGTCT-TAGCGGCGTTTGTATA
1 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* * * *
24548 AAAAACGCTC-CTAAAGTATGATTCTATAGCGGAGTTTGTGT-
1 AAAAACGC-CACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* * *
24589 AAAAACGCCACTATAGTACTAGTCTTTAGCGGCGTTTGTATA
1 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* * * * * *
24631 CAAAA-GCCACTAAAGTAAGA-TCTTTTGCGGCCTTTTTAT-
1 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* *
24670 ACAAACGCCTCTAAAGT
1 AAAAACGCCACTAAAGT
24687 TAGATCTTTT
Statistics
Matches: 322, Mismatches: 46, Indels: 38
0.79 0.11 0.09
Matches are distributed among these distances:
39 3 0.01
40 101 0.31
41 100 0.31
42 77 0.24
43 41 0.13
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (42 bp):
AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
Found at i:24642 original size:205 final size:206
Alignment explanation
Indices: 24301--24678 Score: 516
Period size: 205 Copynumber: 1.8 Consensus size: 206
24291 GTTTGTAAAC
24301 AAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTAAAAAATACCACTAAAGTACGAGTCT
1 AAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTAAAAAATACCACTAAAGTACGAGTCT
*
24366 ATAGCGGCGTTTATAAAAAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAAAAAC
66 ATAGCGGAGTTTATAAAAAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAAAAAC
* *
24431 GCCACTAAAGTATGAGT-TATAGCGGCGTTTTTATACAAACGCCACTACAGTACGACTTATAACA
131 GCCACTAAAGTAAGA-TCTATAGCGGCCTTTTTATACAAACGCCACTACAGTACGACTTATAACA
24495 GTGCTTTTATAA
195 GTGCTTTTATAA
* * * * *
24507 AAAAACGCCACTAAAGTACGAGTC-TTAGCGGCGTTTGTATAAAAA-ACGCTCCTAAAGTATGAT
1 AAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTA-AAAAATAC-C-ACTAAAGTACGAG
* ** * * * *
24570 TCTATAGCGGAGTTTGT-GTAAAAA-CGCCACTATAGTACTAGTCTTTAGCGGCGTTTGTATACA
63 TCTATAGCGGAGTTTATAAAAAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATA-A
* *
24633 AAA-GCCACTAAAGTAAGATCTTTTGCGGCCTTTTTATACAAACGCC
127 AAACGCCACTAAAGTAAGATCTATAGCGGCCTTTTTATACAAACGCC
24679 TCTAAAGTTA
Statistics
Matches: 150, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
204 1 0.01
205 87 0.58
206 37 0.25
207 25 0.17
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (206 bp):
AAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTAAAAAATACCACTAAAGTACGAGTCT
ATAGCGGAGTTTATAAAAAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAAAAAC
GCCACTAAAGTAAGATCTATAGCGGCCTTTTTATACAAACGCCACTACAGTACGACTTATAACAG
TGCTTTTATAA
Found at i:24661 original size:123 final size:121
Alignment explanation
Indices: 24259--24686 Score: 379
Period size: 124 Copynumber: 3.5 Consensus size: 121
24249 GCATTTGTTT
* * * * * *
24259 AAAAATGCCACTAAAGTACAAGT-TTATAGC-GCGTTTGTAAACAAAAACGCCACGAAAGAACGA
1 AAAAACGCCACTAAAGTACGAGTCTT-TAGCGGCGTTTGT--ATAAAAACGCCACTAAAGTATGA
* * ** * *
24322 GTCTTTAGCGGCGTTTGTA-AAAAATACCACTAAAGTACGAGTCTATAGCGGCGTTTATAAA
63 GT-TATAGCGGAGTTTGTATAAAAACGCCACTAAAGTAC-AGTCTTTAGCGGCGTTT-TATA
* *
24383 AAAAATCGCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAAAAACGCCACTAAAGTATGAGT
1 AAAAA-CGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGT
* * * * * *
24448 TATAGCGGCGTTTTTATACAAACGCCACTACAGTAC-GACTTATAACAGTGC-TTTTATAA
65 TATAGCGGAGTTTGTATAAAAACGCCACTAAAGTACAGTCTT-TAGC-G-GCGTTTTAT-A
*
24507 AAAAACGCCACTAAAGTACGAGTC-TTAGCGGCGTTTGTATAAAAAACGCTC-CTAAAGTATGAT
1 AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT-AAAAACGC-CACTAAAGTATGAG
* *
24570 TCTATAGCGGAGTTTGTGTAAAAACGCCACTATAGTACTAGTCTTTAGCGGCGTTTGTATA
64 T-TATAGCGGAGTTTGTATAAAAACGCCACTAAAGTAC-AGTCTTTAGCGGCGTTT-TATA
* * * * * * *
24631 CAAAA-GCCACTAAAGTAAGA-TCTTTTGCGGCCTTTTTATACAAACGCCTCTAAAGT
1 AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGT
24687 TAGATCTTTT
Statistics
Matches: 253, Mismatches: 34, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
121 1 0.00
122 33 0.13
123 87 0.34
124 92 0.36
125 28 0.11
126 12 0.05
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (121 bp):
AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTT
ATAGCGGAGTTTGTATAAAAACGCCACTAAAGTACAGTCTTTAGCGGCGTTTTATA
Found at i:24671 original size:40 final size:40
Alignment explanation
Indices: 24508--24701 Score: 135
Period size: 41 Copynumber: 4.8 Consensus size: 40
24498 CTTTTATAAA
* * * *
24508 AAAACGCCACTAAAGTACGAGTC-TTAGCGGCGTTTGTATAA
1 AAAA-GCCACTAAAGTAAGA-TCTTTTGCGGCCTTTGTATAC
* * * ** *
24549 AAAACGCTC-CTAAAGTATGATTCTATAGCGGAGTTTGTGTA-
1 AAAA-GC-CACTAAAGTAAGA-TCTTTTGCGGCCTTTGTATAC
* * *
24590 AAAACGCCACTATAGTACTAG-TCTTTAGCGGCGTTTGTATAC
1 AAAA-GCCACTAAAGTA--AGATCTTTTGCGGCCTTTGTATAC
*
24632 AAAAGCCACTAAAGTAAGATCTTTTGCGGCCTTTTTATAC
1 AAAAGCCACTAAAGTAAGATCTTTTGCGGCCTTTGTATAC
* * *
24672 AAACGCCTCTAAAGTTAGATCTTTTGCGGC
1 AAAAGCCACTAAAGTAAGATCTTTTGCGGC
24702 ATTTATTCAA
Statistics
Matches: 129, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
39 2 0.02
40 46 0.36
41 61 0.47
42 19 0.15
43 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (40 bp):
AAAAGCCACTAAAGTAAGATCTTTTGCGGCCTTTGTATAC
Found at i:25048 original size:17 final size:17
Alignment explanation
Indices: 25022--25056 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25012 AAACTCTAAC
*
25022 TCAAAATTTAAATTATT
1 TCAAAATTTAAAATATT
*
25039 TCAAATTTTAAAATATT
1 TCAAAATTTAAAATATT
25056 T
1 T
25057 TATTTGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
TCAAAATTTAAAATATT
Found at i:25071 original size:21 final size:22
Alignment explanation
Indices: 25034--25076 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
25024 AAAATTTAAA
25034 TTATTTCAAATTTTAAAATATT
1 TTATTTCAAATTTTAAAATATT
*
25056 TTATTTGAAA-TTTAAAATATT
1 TTATTTCAAATTTTAAAATATT
25077 AGATATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTTCAAATTTTAAAATATT
Found at i:28857 original size:22 final size:22
Alignment explanation
Indices: 28829--28882 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
28819 CCAAAATAAT
28829 AATAAAAATATTATTTTTATTC
1 AATAAAAATATTATTTTTATTC
* *
28851 AATAAAAACATTATTTTTATTT
1 AATAAAAATATTATTTTTATTC
*
28873 AATGAAAATA
1 AATAAAAATA
28883 ATGATTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
AATAAAAATATTATTTTTATTC
Found at i:28889 original size:23 final size:22
Alignment explanation
Indices: 28828--28889 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
28818 CCCAAAATAA
28828 TAATAAAA-ATATTATTTTTATT
1 TAATAAAATA-ATTATTTTTATT
*
28850 CAATAAAA-ACATTATTTTTATT
1 TAATAAAATA-ATTATTTTTATT
*
28872 TAATGAAAATAATGATTT
1 TAAT-AAAATAATTATTT
28890 AATTGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.68
23 10 0.29
24 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (22 bp):
TAATAAAATAATTATTTTTATT
Found at i:30804 original size:17 final size:16
Alignment explanation
Indices: 30784--30816 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
30774 AAGAGCTGTT
30784 TTTTTAATAAAAAATTA
1 TTTTTAA-AAAAAATTA
30801 TTTTTAAAAAAAATTA
1 TTTTTAAAAAAAATTA
30817 AAATAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTTAAAAAAAATTA
Found at i:32862 original size:157 final size:155
Alignment explanation
Indices: 32626--33194 Score: 664
Period size: 156 Copynumber: 3.6 Consensus size: 155
32616 CCTAATTTCA
** * * * * *
32626 TTATTTCTTCAATTTTTCCTTCATTTTAAGTCTATTTTCTACCAAATTTAAACCACATGCTCGTA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTATTTT-TACCAAATTTGAGCCACATGCTCCTA
* *
32691 AACCATAGTAGAATAAATGTGTATTTTCAATTCCTCTATTTGATATCAAATTTTTTATTTTTCAA
65 AACCATAGTAGAATACATGTGTACTTTCAATTCCTCT-TTTGATATCAAATTTTTTATTTTTCAA
32756 TTTAGTCCTTCAAGTTTTCATAATCTCC
129 TTTAGTCCTTCAA-TTTTCATAATCTCC
* **
32784 TTATTTCTTCAATTCGTCATTTATTTTAATTCTATTTTTACCAAATTTGAGTGACATGCTCCTAA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTATTTTTACCAAATTTGAGCCACATGCTCCTAA
** * *
32849 AAAATAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAAATTTTTTATTTTTCAAT
66 ACCATAGTAGAATACATGTGTACTTTCAATTCCTC-TTTTGATATCAAATTTTTTATTTTTCAAT
32914 TTAGTCCTTCAATTTTCATAATCTCAC
130 TTAGTCCTTCAATTTTCATAATCTC-C
*
32941 -TATTTCTTCAATTCGTCATTTATTTTAAGTCTGA-TTTTATCAAATTTGAGCCACATGCTCCTA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCT-ATTTTTACCAAATTTGAGCCACATGCTCCTA
* *
33004 AACCATAGTAGAATACATCTGTACTTTCAATTCCTCTTTT-TTAT-AATATGTTTTTATTTTT-A
65 AACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTGATATCAA-AT-TTTTTATTTTTCA
33066 ATTTAGTCCTTCAATTTTTCATAATCTCC
128 ATTTAGTCCTTCAA-TTTTCATAATCTCC
* * ** * * * * **
33095 TTATTCCATCCGTTTGTGATTTATTTTAAGTCCTTGTTTTTCTACCAAATTTGAACCATGTGCTC
1 TTATTTCTTCAATTCGTCATTTATTTTAAGT-C-T-ATTTT-TACCAAATTTGAGCCACATGCTC
* * * * *
33160 ATATACCACAATAGAATACATATGTAAC-TTCAATT
62 CTAAACCATAGTAGAATACATGTGT-ACTTTCAATT
33195 TTTATTTTTT
Statistics
Matches: 357, Mismatches: 42, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
153 2 0.01
154 20 0.06
155 52 0.15
156 103 0.29
157 95 0.27
158 37 0.10
159 46 0.13
160 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (155 bp):
TTATTTCTTCAATTCGTCATTTATTTTAAGTCTATTTTTACCAAATTTGAGCCACATGCTCCTAA
ACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTGATATCAAATTTTTTATTTTTCAATT
TAGTCCTTCAATTTTCATAATCTCC
Found at i:38738 original size:199 final size:198
Alignment explanation
Indices: 38398--38783 Score: 449
Period size: 199 Copynumber: 1.9 Consensus size: 198
38388 TATAGGCATG
* * * *
38398 TTCGGGTATTTAATCTCAAAATTTTCGTAATTTATAAGATTAGAAGAGTAGTATTGGAATTTATC
1 TTCGGGTAGTTAATCTCAAAATTTTCATAATTTATAAGATTAGAAGAGTAGTATTGGAACTAATC
* * * * *** *
38463 TTTCAGTTGAGGCAATATCGAGACATACGAGATATTGTAAACATGTTAAAAATCGTGTTGAAAAT
66 TTTCAGTTGAGGCAATATCGACACATACGAGACATTGTAAACAGGATAAAAATCACATTCAAAAT
*
38528 GATTCCAAAGCTT-GTTTTGTGCAAGAATAAAAAGATACAAAATAG-CTTGATAGACATGTTCGG
131 GATTCCAAAGCTTGGTTTTGTGCAAGAAGAAAAAGAT--AAAAT-GCCTTGATAGACATGTTCGG
38591 GGTATT
193 GGTATT
* * * *
38597 TTCGGGTAGTTAATCT-AAATTTTTTCATAATTTATAAGATTATAAGTGTAGTATTGGTACTAAT
1 TTCGGGTAGTTAATCTCAAA-ATTTTCATAATTTATAAGATTAGAAGAGTAGTATTGGAACTAAT
* * ***
38661 CTTTCAGTTGAGGTTAATATTGACACATA-GAGACATTGTAAGTGGGATAAAAATCACATTCAAA
65 CTTTCAGTTGAGG-CAATATCGACACATACGAGACATTGTAAACAGGATAAAAATCACATTCAAA
* * * *
38725 GTGGA-TCCAAAGCTTGGTTTTGTGCATGAAGAACAAGCTAAAATGCCTTGATAGACATG
129 AT-GATTCCAAAGCTTGGTTTTGTGCAAGAAGAAAAAGATAAAATGCCTTGATAGACATG
38784 ACTAGTATCG
Statistics
Matches: 156, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
197 1 0.01
198 21 0.13
199 101 0.65
200 33 0.21
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (198 bp):
TTCGGGTAGTTAATCTCAAAATTTTCATAATTTATAAGATTAGAAGAGTAGTATTGGAACTAATC
TTTCAGTTGAGGCAATATCGACACATACGAGACATTGTAAACAGGATAAAAATCACATTCAAAAT
GATTCCAAAGCTTGGTTTTGTGCAAGAAGAAAAAGATAAAATGCCTTGATAGACATGTTCGGGGT
ATT
Found at i:40490 original size:24 final size:23
Alignment explanation
Indices: 40454--40535 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 23
40444 ATTCGAATAT
* *
40454 TAAAGAAAATGGAGTTCGGTTAAC
1 TAAA-AAAATGGAGTTAGATTAAC
40478 TAAAAAAATTGGAGTTAGATTAAC
1 TAAAAAAA-TGGAGTTAGATTAAC
*
40502 TAAAAAAGAAAATGGAGTTTGATTAAC
1 T---AAA-AAAATGGAGTTAGATTAAC
40529 TAAAAAA
1 TAAAAAA
40536 TTACAAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 7 0.14
24 21 0.42
27 18 0.36
28 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (23 bp):
TAAAAAAATGGAGTTAGATTAAC
Found at i:40525 original size:27 final size:27
Alignment explanation
Indices: 40455--40535 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
40445 TTCGAATATT
* *
40455 AAAGAAAATGGAGTTCGGTTAACT--A
1 AAAGAAAATGGAGTTAGATTAACTAAA
*
40480 AAA-AAATTGGAGTTAGATTAACTAAA
1 AAAGAAAATGGAGTTAGATTAACTAAA
*
40506 AAAGAAAATGGAGTTTGATTAACTAAA
1 AAAGAAAATGGAGTTAGATTAACTAAA
40533 AAA
1 AAA
40536 TTACAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 17 0.35
25 3 0.06
26 4 0.08
27 24 0.50
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.25
Consensus pattern (27 bp):
AAAGAAAATGGAGTTAGATTAACTAAA
Found at i:40894 original size:36 final size:36
Alignment explanation
Indices: 40826--40894 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
40816 CCAACACTCC
* * *
40826 CCCTCCCTCAGCTGGCCCAGCACCCCAGCCCCACCT
1 CCCTCCCTAAGCTGGCCCAACACCCCAACCCCACCT
*
40862 CCCTCCCTAAGTTGGCCCAAC-CTCCCAACCCCA
1 CCCTCCCTAAGCTGGCCCAACAC-CCCAACCCCA
40895 GAGCCTATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 1 0.04
36 27 0.96
ACGTcount: A:0.17, C:0.58, G:0.12, T:0.13
Consensus pattern (36 bp):
CCCTCCCTAAGCTGGCCCAACACCCCAACCCCACCT
Found at i:41650 original size:27 final size:27
Alignment explanation
Indices: 41598--41650 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
41588 TCCGGAGGCT
* * *
41598 CCATATGATGAAATGTTGACTGAGTCA
1 CCATATGATGAAATGCTAACTAAGTCA
*
41625 CCATATGTTGAAATGCTAACTAAGTC
1 CCATATGATGAAATGCTAACTAAGTC
41651 GAGTGGGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (27 bp):
CCATATGATGAAATGCTAACTAAGTCA
Found at i:43293 original size:4 final size:4
Alignment explanation
Indices: 43286--43381 Score: 57
Period size: 4 Copynumber: 22.8 Consensus size: 4
43276 CCCTTCAATC
* ** * * * *
43286 AAAT AAAT AAAT AAAT AATTT ATTT GAAAC AAAT GAAT ATAG AAAT AAAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
* * *
43336 AAAT GATT CAAAAT AAAT AAAT AATT CAAAT AAAT AAAT AAAT AAA
1 AAAT AAAT --AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAA
43382 ATTACTTCTA
Statistics
Matches: 69, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
4 61 0.88
5 6 0.09
6 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:43368 original size:13 final size:12
Alignment explanation
Indices: 43346--43381 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
43336 AAATGATTCA
43346 AAATAAATAAAT
1 AAATAAATAAAT
*
43358 AATTCAAATAAAT
1 AAAT-AAATAAAT
43371 AAATAAATAAA
1 AAATAAATAAA
43382 ATTACTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:43380 original size:21 final size:18
Alignment explanation
Indices: 43328--43376 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
43318 ATGAATATAG
*
43328 AAATAAATAAATGATTCA
1 AAATAAATAAATAATTCA
43346 AAATAAATAAATAATTC-
1 AAATAAATAAATAATTCA
43363 AAATAAATAAATAA
1 AAATAAATAAATAA
43377 ATAAAATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAAATAAATAATTCA
Found at i:43383 original size:17 final size:17
Alignment explanation
Indices: 43290--43383 Score: 80
Period size: 18 Copynumber: 5.2 Consensus size: 17
43280 TCAATCAAAT
*
43290 AAATAAATAAATAATTT
1 AAATAAATAAATAATTA
** *
43307 ATTTGAAACAAATGAATATA
1 AAAT-AAATAAAT-AAT-TA
*
43327 GAAATAAATAAATGATTCA
1 -AAATAAATAAATAATT-A
*
43346 AAATAAATAAATAATTC
1 AAATAAATAAATAATTA
*
43363 AAATAAATAAATAAATA
1 AAATAAATAAATAATTA
43380 AAAT
1 AAAT
43384 TACTTCTATA
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
17 21 0.35
18 23 0.38
19 6 0.10
20 8 0.13
21 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (17 bp):
AAATAAATAAATAATTA
Found at i:43971 original size:31 final size:29
Alignment explanation
Indices: 43904--43978 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
43894 ATTTTATAAG
*
43904 CTAATTT-TTATTATATTATAATCATTTA
1 CTAATTTATTATTTTATTATAATCATTTA
* * *
43932 ATAATTTATTATTTTATTATATTTTATTGTA
1 CTAATTTATTATTTTATTATA-ATCATT-TA
43963 CTAATTTATTACTTTT
1 CTAATTTATTA-TTTT
43979 TGTAGTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 6 0.16
29 12 0.32
30 4 0.11
31 12 0.32
32 4 0.11
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (29 bp):
CTAATTTATTATTTTATTATAATCATTTA
Found at i:46049 original size:41 final size:41
Alignment explanation
Indices: 45995--46103 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
45985 CTTATTTTTA
*
45995 TTTA-TTTTGTTTCTTAATGTTTTTATTTAATTATGTACTT
1 TTTATTTTTGTTTCTTAATGTTTTTATTTAATTATGGACTT
*
46035 TTTATTTTTGTTTCTTAATG-TTTTATTTAATTATGGGCTT
1 TTTATTTTTGTTTCTTAATGTTTTTATTTAATTATGGACTT
*
46075 TTTTTATTTTGTTTCTTAATGTTTTTATT
1 TTTAT-TTTTGTTTCTTAATGTTTTTATT
46104 ATTTAATTGT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
40 26 0.41
41 30 0.48
42 7 0.11
ACGTcount: A:0.17, C:0.05, G:0.09, T:0.69
Consensus pattern (41 bp):
TTTATTTTTGTTTCTTAATGTTTTTATTTAATTATGGACTT
Found at i:46060 original size:21 final size:21
Alignment explanation
Indices: 45995--46062 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
45985 CTTATTTTTA
45995 TTTA-TTTTGTTTCTTAATGT
1 TTTATTTTTGTTTCTTAATGT
* ** * *
46015 TTT-TATTTAATTATGTACT-T
1 TTTATTTTTGTTTCT-TAATGT
46035 TTTATTTTTGTTTCTTAATGT
1 TTTATTTTTGTTTCTTAATGT
46056 TTTATTT
1 TTTATTT
46063 AATTATGGGC
Statistics
Matches: 34, Mismatches: 10, Indels: 7
0.67 0.20 0.14
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (21 bp):
TTTATTTTTGTTTCTTAATGT
Done.